Form and Function of Proteins. Historical Background and the Indian Effort in Macromolecular Crystallography

Global efforts in macromolecular crystallography started in the thirties of the last century. However, definitive results began to emerge only in the late fifties and the early sixties. India has a long tradition in crystallography. The country had a head start in theoretical and computational structural biology, thanks to the efforts of G.N. Ramachandran and his colleagues in the fifties and the sixties. However, macromolecular crystallography got off the ground in India only in the eighties, particularly after the Bangalore group received adequate support from the Department of Science and Technology under their Thrust Area Programme. The Bangalore centre was also identified as a national nucleus for the development of the area in the country. Since then work in the area has spread widely and is being carried out by several groups, mainly led by scientists trained at Bangalore or their descendents, in about thirty institutions in India. In addition to the Department of Science and Technology, the effort is now supported by other agencies like the Department of Biotechnology and the Council of Scientific and Industrial Research. The problems addressed by macromolecular crystallographers in India encompass almost all aspects of modern biology. Indian efforts in macromolecular crystallography have also become an important component of the international efforts in the area.

Levels of Alpha-Toxin Correlate with Distinct Phenotypic Response Profiles of Blood Mononuclear Cells and with agr Background of Community-Associated Staphylococcus aureus Isolates

Epidemiological studies of Staphylococcus aureus have shown a relation between certain clones and the presence of specific virulence genes, but how this translates into virulence-associated functional responses is not fully elucidated. Here we addressed this issue by analyses of community-acquired S. aureus strains characterized with respect to antibiotic resistance, ST types, agr types, and virulence gene profiles. Supernatants containing exotoxins were prepared from overnight bacterial cultures, and tested in proliferation assays using human peripheral blood mononuclear cells (PBMC). The strains displayed stable phenotypic response profiles, defined by either a proliferative or cytotoxic response. Although, virtually all strains elicited superantigen-mediated proliferative responses, the strains with a cytotoxic profile induced proliferation only in cultures with the most diluted supernatants. This indicated that the superantigen-response was masked by a cytotoxic effect which was also confirmed by flow cytometry analysis. The cytotoxic supernatants contained significantly higher levels of alpha-toxin than did the proliferative supernatants. Addition of alpha-toxin to supernatants characterized as proliferative switched the response into cytotoxic profiles. In contrast, no effect of Panton Valentine Leukocidin, delta-toxin or phenol soluble modulin alpha-3 was noted in the proliferative assay. Furthermore, a significant association between agr type and phenotypic profile was found, where agrII and agrIII strains had predominantly a proliferative profile whereas agrI and IV strains had a predominantly cytotoxic profile. The differential response profiles associated with specific S. aureus strains with varying toxin production could possibly have an impact on disease manifestations, and as such may reflect specific pathotypes.

Simultaneously Uncovering the Patterns of Brain Regions Involved in Different Story Reading Subprocesses

Story understanding involves many perceptual and cognitive subprocesses, from perceiving individual words, to parsing sentences, to understanding the relationships among the story characters. We present an integrated computational model of reading that incorporates these and additional subprocesses, simultaneously discovering their fMRI signatures. Our model predicts the fMRI activity associated with reading arbitrary text passages, well enough to distinguish which of two story segments is being read with 74% accuracy. This approach is the first to simultaneously track diverse reading subprocesses during complex story processing and predict the detailed neural representation of diverse story features, ranging from visual word properties to the mention of different story characters and different actions they perform. We construct brain representation maps that replicate many results from a wide range of classical studies that focus each on one aspect of language processing and offer new insights on which type of information is processed by different areas involved in language processing. Additionally, this approach is promising for studying individual differences: it can be used to create single subject maps that may potentially be used to measure reading comprehension and diagnose reading disorders.

SARAS MEASUREMENT OF THE RADIO BACKGROUND AT LONG WAVELENGTHS

SARAS is a correlation spectrometer connected to a frequency independent antenna that is purpose-designed for precision measurements of the radio background at long wavelengths. The design, calibration, and observing strategies admit solutions for the internal additive contributions to the radiometer response, and hence a separation of these contaminants from the antenna temperature. We present here a wideband measurement of the radio sky spectrum by SARAS that provides an accurate measurement of the absolute brightness and spectral index between 110 and 175MHz. Accuracy in the measurement of absolute sky brightness is limited by systematic errors of magnitude 1.2%; errors in calibration and in the joint estimation of sky and system model parameters are relatively smaller. We use this wide-angle measurement of the sky brightness using the precision wide-band dipole antenna to provide an improved absolute calibration for the 150 MHz all-sky map of Landecker and Wielebinski: subtracting an offset of 21.4 K and scaling by a factor of 1.05 will reduce the overall offset error to 8 K (from 50 K) and scale error to 0.8% (from 5%). The SARAS measurement of the temperature spectral index is in the range -2.3 to -2.45 in the 110-175MHz band and indicates that the region toward the Galactic bulge has a relatively flatter index.

Energy Harvesting WSNs for Accurately Estimating the Maximum Sensor Reading: Trade-Offs and Optimal Design

Computing the maximum of sensor readings arises in several environmental, health, and industrial monitoring applications of wireless sensor networks (WSNs). We characterize the several novel design trade-offs that arise when green energy harvesting (EH) WSNs, which promise perpetual lifetimes, are deployed for this purpose. The nodes harvest renewable energy from the environment for communicating their readings to a fusion node, which then periodically estimates the maximum. For a randomized transmission schedule in which a pre-specified number of randomly selected nodes transmit in a sensor data collection round, we analyze the mean absolute error (MAE), which is defined as the mean of the absolute difference between the maximum and that estimated by the fusion node in each round. We optimize the transmit power and the number of scheduled nodes to minimize the MAE, both when the nodes have channel state information (CSI) and when they do not. Our results highlight how the optimal system operation depends on the EH rate, availability and cost of acquiring CSI, quantization, and size of the scheduled subset. Our analysis applies to a general class of sensor reading and EH random processes.

Estimation of background carrier concentration in fully depleted GaN films

Buffer leakage is an important parasitic loss mechanism in AlGaN/GaN high electron mobility transistors (HEMTs) and hence various methods are employed to grow semi-insulating buffer layers. Quantification of carrier concentration in such buffers using conventional capacitance based profiling techniques is challenging due to their fully depleted nature even at zero bias voltages. We provide a simple and effective model to extract carrier concentrations in fully depleted GaN films using capacitance-voltage (C-V) measurements. Extensive mercury probe C-V profiling has been performed on GaN films of differing thicknesses and doping levels in order to validate this model. Carrier concentrations as extracted from both the conventional C-V technique for partially depleted films having the same doping concentration, and Hall measurements show excellent agreement with those predicted by the proposed model thus establishing the utility of this technique. This model can be readily extended to estimate background carrier concentrations from the depletion region capacitances of HEMT structures and fully depleted films of any class of semiconductor materials.

Tropical river fisheries valuation: background papers to a global synthesis

This report is a compilation of five regional reviews that document the global status of tropical rivers and inland fisheries in three continents: Latin America, Africa and Asia. It explores the role of ‘valuation’ methods and their contribution to policy-making and river fishery management. From the compilation, the best estimate of the global value of inland fisheries for those three continents is US$ 5.58 billion (gross market value), which is equivalent to 19 percent of the current value of annual fish exports from developing countries (US$ 29 billion) for 2004. The compilation shows that there is a general shortage of information on inland fisheries, especially derived from conventional economic valuation methods, though information from economic impact assessment methods and socio-economic and livelihood analysis methods is more widely available. The status of knowledge about the impact of changes in river management on the value of tropical river fisheries is weak and patchy. Although the impacts of large dams on the hydrology, ecology and livelihood support attributes of tropical rivers are well-recognized, there have been only few valuation studies of these issues. The document highlights the need for further valuation studies of tropical river and inland fisheries in developing countries. It underlines how vital it is for policy-makers and other stakeholders to understand the importance of these natural resources in order to make appropriate decisions concerning their role in development policy and illustrates why capacity building in valuation should become a major priority for agencies concerned with fisheries management and policy-making.

Florida's ground water quality monitoring program: background hydrogeochemistry

The purpose of this report is to present the results of the initial quantification of background water quality in each of the state's major potable aquifer systems. Results are presented and interpreted in light of the influencing factors which locally and regionally affect ambient ground-water quality. This initial data will serve as a baseline from which future sampling results can be compared. Future sampling of the Network will indicate the extent to which Florida's regional ground-water resources are improving or declining in quality. (Document has 378 pages.)